Error in toolshed error message

[s.mukundan@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
It said that 'angle' command was only available in uninstalled package seqcrow. So I tried to install  seqcrow and got this message.

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:\\\Users\\\ASUS\\\home_gourd\\\Protein_grafter\\\dev\\\post_rot.pdb

> open C:/Users/ASUS/home_gourd/Protein_grafter/dev/pre_rot.pdb

> close

> open C:\Users\ASUS\home_gourd\Protein_grafter\dev\pre_rot.pdb format pdb

> open C:/Users/ASUS/home_gourd/Protein_grafter/dev/post_rot.pdb

> ui tool show Distances

> select #2/A:1@CG

1 atom, 1 residue, 1 model selected  

> select #1/A:1@CB

1 atom, 1 residue, 1 model selected  
Exactly two atoms must be selected!  

> select clear

> ui mousemode right distance

> select #2/A:1@CG

1 atom, 1 residue, 1 model selected  

> select #1/A:1@CB

1 atom, 1 residue, 1 model selected  

> ui mousemode right distance

> distance #1/A:1@CB #2/A:1@CG

Distance between pre_rot.pdb #1/A MET 1 CB and post_rot.pdb #2/A MET 1 CG:
1.517Å  

> undo

> undo

> ui mousemode right distance

> close

> open C:\Users\ASUS\home_gourd\Protein_grafter\dev\pre_rot.pdb format pdb

> open C:/Users/ASUS/home_gourd/Protein_grafter/dev/post_rot.pdb

> angle #1/A:1 at cg #1/A:1 at cb #2/A:1 at cg

angle is provided by the uninstalled bundle SEQCROW  
Downloading bundle SEQCROW-0.25.2-py3-none-any.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
WARNING: The script send2trash.exe is installed in
'C:\Users\ASUS\AppData\Local\UCSF\ChimeraX\Python37\Scripts' which is not on
PATH.  
Consider adding this directory to PATH or, if you prefer to suppress this
warning, use --no-warn-script-location.  
WARNING: You are using pip version 20.2.2; however, version 21.2.4 is
available.  
You should consider upgrading via the 'D:\Program Files\ChimeraX
1.1\bin\ChimeraX.exe -m pip install --upgrade pip' command.  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing c:\users\asus\downloads\seqcrow-0.25.2-py3-none-any.whl  
Requirement already satisfied: scipy in d:\program files\chimerax
1.1\bin\lib\site-packages (from SEQCROW==0.25.2) (1.4.1)  
Requirement already satisfied: ChimeraX-Core~=1.1 in d:\program files\chimerax
1.1\bin\lib\site-packages (from SEQCROW==0.25.2) (1.1)  
Collecting Send2Trash  
Downloading Send2Trash-1.8.0-py3-none-any.whl (18 kB)  
Requirement already satisfied: numpy>=1.13.3 in d:\program files\chimerax
1.1\bin\lib\site-packages (from scipy->SEQCROW==0.25.2) (1.18.5+mkl)  
Installing collected packages: Send2Trash, SEQCROW  
Successfully installed SEQCROW-0.25.2 Send2Trash-1.8.0  
Lock 2495021411848 acquired on
C:\Users\ASUS\AppData\Local\UCSF\ChimeraX\Cache\1.1\toolshed\bundle_info.cache.lock  
Lock 2495021411848 released on
C:\Users\ASUS\AppData\Local\UCSF\ChimeraX\Cache\1.1\toolshed\bundle_info.cache.lock  
\---  

Successfully installed SEQCROW-0.25.2 Send2Trash-1.8.0  
Installed SEQCROW (0.25.2)  
resumed SEQCROW queue  
adding Gaussian format  
adding ORCA format  
adding Psi4 format  
adding Gaussian format  
adding ORCA format  
adding Psi4 format  
adding Gaussian format  

local job type Gaussian from SEQCROW supplanted that from SEQCROW  

adding ORCA format  

local job type ORCA from SEQCROW supplanted that from SEQCROW  

adding Psi4 format  

local job type Psi4 from SEQCROW supplanted that from SEQCROW  

adding Gaussian format  

file format Gaussian from SEQCROW supplanted that from SEQCROW  

adding ORCA format  

file format ORCA from SEQCROW supplanted that from SEQCROW  

adding Psi4 format  

file format Psi4 from SEQCROW supplanted that from SEQCROW  

> angle #1/A:1 at cg #1/A:1 at cb #2/A:1 at cg

angle is provided by the uninstalled bundle SEQCROW  

> ui mousemode right minimize

> ui mousemode right minimize

> ui mousemode right select

> select #1/A:1@CG

1 atom, 1 residue, 1 model selected  

> ui mousemode right rotate

Downloading bundle SEQCROW-0.25.2-py3-none-any.whl  
Traceback (most recent call last):  
File "D:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\help_viewer\tool.py", line 389, in download_finished  
session=self.session)  
File "D:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 903, in install_bundle  
_install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall,
session=session, no_deps=no_deps)  
File "D:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\toolshed_utils\\__init__.py", line 213, in _install_bundle  
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)  
AttributeError: 'str' object has no attribute 'name'  
  
AttributeError: 'str' object has no attribute 'name'  
  
File "D:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\toolshed_utils\\__init__.py", line 213, in _install_bundle  
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 456.71
OpenGL renderer: GeForce GTX 1050 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUSTeK COMPUTER INC.
Model: Strix 15 GL503GE
OS: Microsoft Windows 10 Home Single Language (Build 19043)
Memory: 17,027,031,040
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-8750H CPU @ 2.20GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    gdcm: 2.8.8
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5+mkl
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pywin32: 228
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    Send2Trash: 1.8.0
    SEQCROW: 0.25.2
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2
    WMI: 1.5.1

[Eric Pettersen]

Hi,

Thanks for reporting this problem. Please upgrade to the 1.2 release or the daily build. This problem has been fixed and also the 'angle' command is provided as a builtin ChimeraX command.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab